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Patrick Jane finally comes face-to-face with Red John, the serial killer he's tracked since the man murdered his wife and daughter. For 10 years, Jane has doggedly hunted his nemesis in his search for justice.

Lisbon walks into an almost empty office that is currently being cleared out, in order to meet with Abbott along with the rest of her team, with the exception of Patrick. Abbott talks to them about their situation and says that the FBI will be talking to each member of the team individually and that they are allowed an attorney. Cho asks why they would need one, and Abbott replies that they might be criminals too, since their boss Bertram is one.

At a gas station, Bertram calls Patrick using a pay-phone while his accomplice Oscar Cordero keeps watch. However, in the middle of his conversation, a police officer who walks in after them identifies Bertram. Before the officer can draw his gun, Bertram’s accomplice shoots him dead. Bertram walks out, leaving the pay phone hanging with Patrick still on the line.

A team is raiding the attic in search of Patrick, but to no avail. Abbott questions Lisbon about Patrick’s whereabouts but she says that she does not know. Lisbon heads to the car park and Rigsby suddenly calls out to her, asking if it is safe. She is surprised when Van Pelt and Cho gets out of the car. Van Pelt says that they are just laying low, since the FBI are looking for them after Bertram’s action at the gas station. Lisbon assures them that there are no arrest warrants for them yet. Van Pelt asks where Jane is and Lisbon tells them that they don't want to know, and that she is not their boss any more. However, Cho still asks where Jane is.

Patrick is feeding pigeons in a park, when Lisbon walks to him and informs him that Abbott has put out a warrant on him. Patrick does not really care and tells Lisbon about Bertram’s phone call. He is expecting Bertram to call him back since their conversation was interrupted. Patrick is aware of the trace the FBI have on his phone, but he cannot get rid of it until he receives the call. Lisbon wonders what Bertram wants and says that Patrick knows. At this moment, his cell rings. Bertram is at the other end. Patrick tells him that his phone is not safe and says that he will call him back. He approaches a cyclist and trades three hundred dollars and his phone for the cyclist’s phone. Patrick calls Bertram and they arrange a meeting. At first Patrick rejects Bertram's proposed meeting place and suggests a bus station. Bertram says it is too public so Patrick compromises and asks if Bertram knows the secluded church by Alexandria Cemetery. Bertram replies, "Of course" (it is where Patrick's family is buried). Lisbon tells Patrick that it is a trap and tries to dissuade him from going, saying that Bertram will be arrested by the FBI sooner or later. However, Patrick does not want that to happen. He rejects her offer to accompany him and asks to borrow her gun, saying that he will use it as a prop. Lisbon gives Jane both her gun and her car key.

On her way, Lisbon sees two officers talking to the cyclist that Patrick previously approached. Patrick drives away before the officers can get him. However, he is soon trapped by other police cars. With many officers pointing guns at him, Patrick leaves the car that he borrowed from Lisbon, and gets on the ground. He tries to ask Abbott for an hour, promising to turn himself in afterwards but changes his mind. Lisbon approaches and asks Abbott for a favor, swearing that she will bring Patrick back later. However, Abbott refuses. Abbott catches on to their urgency and deduces that they made a plan with Bertram. Cho, Rigsby, and Van Pelt arrive and Cho tells Abbott to let Patrick go. However, Abbott says that there is no CBI and tells them that they are impersonating officers of the law. The team questions if Abbott is a member of The Blake Association and tell him to prove that he is not. Lisbon says that since Smith is a member, Abbott could be too. Therefore, it is their duty to protect Jane from harm. Abbott takes a step towards Lisbon, but the team draws their guns. Abbott lets Patrick go, and arrests the team. He reveals that a bug was placed on Lisbon’s car, saying that it was the reason they found Patrick.

Patrick sees the police car behind him. After shaking them off for a bit, he drives to a diner and asks some guys to take care of his car for him before disappearing around a corner. However, the guys make off with the car. He hides behind a tree when he sees the police car following Lisbon’s car. When they are gone, he attempts to stop a car passing by, asking for a ride. He is only successful on his second try.

The team and Abbott are in a police car. Abbott gets a report about a sighting of Lisbon’s car. However, the officer reports that the car contains some kids instead of Jane, and that they lost him. Abbott asks the team where Jane went, but Lisbon and Rigsby honestly answer him that they do not know. Abbott gets out of the car, and Cho is pissed that Rigsby is calling Abbott ‘sir’.

Patrick arrives at the meeting place. Before he can enter, he is stopped by Bertram's accomplice Cordero. Cordero says that he needs to search Patrick for weapons, and finds a gun. After he takes it, Jane is free to enter. Bertram is inside waiting for him. He claims that he is not Red John. Patrick checks out the room before sitting down and telling Bertram that he does not believe him. Bertram denies knowledge of Red John when asked, saying that the organization operates on a need-to-know basis. Bertram reveals that he was told to call Patrick, to tell him that the game is over, and to arrange a meeting. Bertram tells Patrick that he is not happy with what is going to happen, and that the association does not like loose ends. Bertram then tells Cordero to shoot Patrick. Bertram mentions how he has always liked Patrick, while Patrick tries to talk the detective down. However, Cordero shoots Bertram instead. Bertram has a quick death. The real Red John then enters the chapel. Red John is Sheriff Thomas McAllister. He asks Oscar to leave. Red John then says hi to Patrick. Patrick says hi in response.

In the car, Van Pelt is frustrated that the FBI is not telling them anything. She quarrels with Rigsby before Lisbon breaks it up. Abbott tells Mullins to get him a paper map of Sacramento.

Red John reveals that he killed Bertram because everyone believes that Bertram is Red John. Thus, it would be a fitting ending if Bertram and Patrick are found dead together as no one would question it. Red John then demonstrates his ability to change his voice. Red John says that he knows Patrick has many questions for him and asks if he wants any answered. However, Patrick replies that he has no questions at all, calling Red John “an evil, sexually perverted sociopath with pathetic delusions of grandeur.” However, Red John does not agree, and admits to creating the secret organization. He says that he has a lot of power in the palm of his hands when nobody even knows who he is.

When Patrick insults him further, Red John comments that he is rude and contemptuous without reason, which is the reason for his wife's and child's death. Red John questions who Patrick is to judge him when he did not know who he is. Patrick replies with nobody. Red John calls him a smart but arrogant man.

Patrick admits that he does not know how Red John had obtained his list of suspects, but he does know how the bomb was pulled off. He says that there were two explosions, a concussion bomb first, followed by a lethal bomb that was only set off after Bertram, Smith and Patrick were dragged out of the way, killing Stiles and Haffner. Red John confirms this. Continuing, Patrick says that Partridge’s job gave him access to the primary DNA database, so he swapped Red John’s DNA with another body that was prepared, which was placed alongside Stiles and Haffner to stage his death.

Patrick asks to show Red John something, and Red John agrees to see it. Patrick places breadcrumbs into Red John's hand before letting out a pigeon which violently attacks Red John, scaring him. Patrick retrieves a hand gun hidden from under a bench in the church and shoots Red John. Cordero rushes in but is shot by Patrick. Patrick tells Red John that the bomb was a mistake because it was too theatrical, so he knew everything that was the opposite must be true.

(This implies that Jane has figured out McAllister was Red John because McAllister was revealed to be startled by pigeons in Wedding in Red after saving Jane from the killer.)

Red John asks not to be killed. Red John says that Patrick is a good man and that the kill will haunt him. However, Patrick is not hesitating, but instead, savoring the moment because he has finally found Red John. Patrick admits to being disappointed.

A woman walks into the church and Red John calls out for help. Patrick says he is a policeman and that she needs to leave, but she does not believe him. Turns out that the woman is with Red John, and she tries to slice Patrick’s throat after getting within distance. Patrick deals with her easily and gets his handgun to chase after Red John.

Abbott is trying to find out where Patrick had arranged to have a meeting with Bertram. After Rigsby confirms that Patrick’s wife was buried at Alexandria Cemetery, the FBI rushes there.

A woman sees the injured Red John and screams for help, alerting Patrick to his location and he gives chase. The FBI is on site and getting ready to enter the place. As Abbott and other FBI officers start searching the area, the woman that previously tried to attack Patrick with a knife, Red John's accomplice, is seen to be hastily making a getaway from the scene, on foot.

Red John breaks through a fence, and crashes through a glass door. Patrick tells the owner of the house that he is the police, and takes the phone from her before giving chase. However, he did not use the phone to communicate with the police and instead, threw it away.

In the church, Abbott finds the body of Bertram. Pretty soon the rest of the FBI force arrives to cordon off the area.

Red John runs towards a creek before succumbing to his wound. Not able to run any further, he collapses to the ground. Patrick walks towards him, as Red John calls 911. Patrick throws Red John's phone away and gets on top of him. Red John tells Patrick not to kill him, telling him that he knew the list because he is real psychic. However, Patrick does not care. He begins to choke Red John and tells him to blink once for no and twice for yes. He asks him if he is sorry for killing his daughter and wife, and Red John blinks twice. Patrick comments that it is good, then Patrick asks him if he is afraid to die, and Red John blinks twice. Patrick then strangles him. Patrick tries to calm himself down and he places the gun in Red John’s hand.

In the empty office, the team is there, along with Mullins. Lisbon’s phone rings. She moves towards it but the agent tells her not to think about it. Patrick leaves Lisbon a message, telling her that it is over as he has finally killed Red John. He is calling to inform her that he is fine, and says that he is going to miss her. Hanging up, he throws away the phone. Patrick walks off before beginning to run away, his quest for vengeance finally over.

This episode will finally show the long-awaited revelation of Red John's true identity, along with his ultimate defeat and death. Also, Red John's net of followers and accomplices (The Blake Association) will come to light, causing ripples throughout law enforcement.